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- PDB-7odq: Neisseria gonorrhoeae transaldolase at 5.4 MGy dose -

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Basic information

Entry
Database: PDB / ID: 7odq
TitleNeisseria gonorrhoeae transaldolase at 5.4 MGy dose
ComponentsTransaldolase
KeywordsTRANSFERASE / TRANSALDOLASE / CROSS-LINK / REGULATION
Function / homology
Function and homology information


transaldolase / transaldolase activity / pentose-phosphate shunt / carbohydrate metabolic process / cytoplasm
Similarity search - Function
Transaldolase type 2 / Transaldolase active site. / Transaldolase, active site / Transaldolase signature 1. / Transaldolase/Fructose-6-phosphate aldolase / Transaldolase/Fructose-6-phosphate aldolase / Aldolase-type TIM barrel
Similarity search - Domain/homology
CITRIC ACID / Transaldolase
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsRabe von Pappenheim, F. / Wensien, M. / Tittmann, K.
CitationJournal: Nat.Chem.Biol. / Year: 2022
Title: Widespread occurrence of covalent lysine-cysteine redox switches in proteins.
Authors: Rabe von Pappenheim, F. / Wensien, M. / Ye, J. / Uranga, J. / Irisarri, I. / de Vries, J. / Funk, L.M. / Mata, R.A. / Tittmann, K.
History
DepositionApr 30, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 13, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transaldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8072
Polymers37,6151
Non-polymers1921
Water7,692427
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area420 Å2
ΔGint2 kcal/mol
Surface area14440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.200, 82.850, 89.420
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Transaldolase /


Mass: 37614.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (bacteria) / Gene: tal, E8M68_10680, WHOO_01512, WHOO_01712 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1D3FXY0, transaldolase
#2: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 427 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.63 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: PEG8000, Sodium citrate, sodium phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.4→38.16 Å / Num. obs: 62051 / % possible obs: 99.1 % / Redundancy: 13.444 % / Biso Wilson estimate: 24.507 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.105 / Rrim(I) all: 0.109 / Χ2: 0.796 / Net I/σ(I): 13.53 / Num. measured all: 834239 / Scaling rejects: 74
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.4-1.4413.3352.4231.0459819454744860.5352.51898.7
1.44-1.4813.5041.8971.3758808445743550.661.9797.7
1.48-1.5213.5131.4571.8357808436442780.741.51498
1.52-1.5713.6691.2052.2756440419041290.8161.25198.5
1.57-1.6213.6240.9352.9455287408240580.8830.97199.4
1.62-1.6713.6220.7833.5453588395839340.9110.81399.4
1.67-1.7413.5580.5914.6751329382037860.9510.61499.1
1.74-1.8113.4920.4575.949180367336450.9720.47599.2
1.81-1.8913.4620.3487.647225354635080.9820.36298.9
1.89-1.9813.3550.25110.3344807339933550.9890.26198.7
1.98-2.0913.1960.17713.9742516323232220.9940.18499.7
2.09-2.2113.1230.12818.8240353308130750.9960.13499.8
2.21-2.3713.8570.10722.7439812287928730.9980.11199.8
2.37-2.5613.7710.0926.7236933268326820.9980.093100
2.56-2.813.5530.07631.1534071251425140.9990.079100
2.8-3.1313.2250.06235.9229716224722470.9990.065100
3.13-3.6113.0280.04843.5926472203220320.9990.05100
3.61-4.4313.2790.04251.1122575172017000.9990.04398.8
4.43-6.2613.2150.04251.3918144137313730.9990.044100
6.26-38.1611.710.03750.6393568247990.9990.03997

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ZX4

6zx4


Resolution: 1.4→38.16 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1724 3098 5 %
Rwork0.1471 58872 -
obs0.1483 61970 99.09 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 92.49 Å2 / Biso mean: 23.5289 Å2 / Biso min: 12.36 Å2
Refinement stepCycle: final / Resolution: 1.4→38.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2645 0 18 434 3097
Biso mean--30.27 33.98 -
Num. residues----352
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4-1.420.37631340.33742593272798
1.42-1.450.35731380.31512621275998
1.45-1.470.31131380.2892602274098
1.47-1.50.29661390.26562622276198
1.5-1.530.29821370.24822616275398
1.53-1.560.24911400.23242651279199
1.56-1.590.2321370.21782627276499
1.59-1.630.2271420.22659280198
1.63-1.670.2151390.185826412780100
1.67-1.710.21571380.17192645278399
1.71-1.760.20911410.15892696283799
1.76-1.820.18411420.147526572799100
1.82-1.890.16021370.13922631276899
1.89-1.960.15991390.13432656279598
1.96-2.050.15671420.125526812823100
2.05-2.160.14451410.116527032844100
2.16-2.290.14651430.115327132856100
2.29-2.470.15391440.119627252869100
2.47-2.720.13741430.122827162859100
2.72-3.110.15661450.133927492894100
3.11-3.920.15811460.12762767291399
3.92-38.160.15641530.14552901305499
Refinement TLS params.Method: refined / Origin x: -13.3627 Å / Origin y: 17.1156 Å / Origin z: -17.6061 Å
111213212223313233
T0.1235 Å20.002 Å2-0.0024 Å2-0.1477 Å2-0.0007 Å2--0.139 Å2
L0.365 °20.0686 °2-0.0025 °2-0.9096 °20.0752 °2--0.4132 °2
S-0.0037 Å °0.0086 Å °-0.0125 Å °0.0001 Å °-0.0036 Å °-0.0184 Å °-0.008 Å °-0.0022 Å °0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA0 - 351
2X-RAY DIFFRACTION1allA401
3X-RAY DIFFRACTION1allS1 - 500

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